Distinguished Speaker Series: Algorithmic challenges in complete genomics and metagenomics
Prof. Pavel Pevzner, Department of Computer Science and Engineering, University of California at San Diego.
Edmond J. Safra Center for Bioinformatics
Distinguished Speaker Series Seminar
Prof. Pavel Pevzner
Department of Computer Science and Engineering, University of California at San Diego
" Algorithmic challenges in complete genomics and metagenomics"
Wednesday, October 19 2022, at 11:15
School of Computer Science, Check Point building, room 420, TAU
Refreshments from 11:00
Abstract: Even though the first draft human genome was generated two decades ago, many biomedically important regions (such as centromeres) represented the terra incognita of the genome sequencing until recently. The long-read DNA sequencing technologies are now transforming genome sequencing toward generating complete genomes and metagenomes. They also raised novel algorithmic challenges that represent the key bottlenecks for the ongoing Vertebrate Genomes Project (aimed at sequencing genomes of all vertebrates) and Human Pangenome Project (aimed at population-scale sequencing of complete human genomes). For example, it turned out that the classical alignment approaches that work well for most sequences, fail to construct biologically adequate alignments of highly repetitive regions, such as centromeres and immunoglobulin loci recently uncovered by complete genomics. I will describe some algorithmic challenges in complete genomics, discuss the recently developed algorithms for their solution, and show how these algorithms bring us closer to the goal of complete genome and metagenome sequencing.
Biosketch: Pavel Pevzner is Ronald R. Taylor Professor of Computer Science and Engineering and Director of the NIH Center for Computational Mass Spectrometry at University of California, San Diego. He holds Ph.D. from Moscow Institute of Physics and Technology, Russia. He was named Howard Hughes Medical Institute Professor in 2006. He was elected the Association for Computing Machinery Fellow in 2010, the International Society for Computational Biology Fellow in 2012, the European Academy of Sciences member (Academia Europaea) in 2016, and the American Association for Advancement in Science (AAAI) Fellow in 2018. He was awarded a Honoris Causa (2011) from Simon Fraser University in Vancouver, the Senior Scientist Award (2017) by the International Society for Computational Biology, and the Kanellakis Theory and Practice Award from the Association for Computing Machinery (2019). Dr. Pevzner authored textbooks "Computational Molecular Biology: An Algorithmic Approach", "Introduction to Bioinformatics Algorithms" (with Neal Jones), “Bioinformatics Algorithms: an Active Learning Approach” (with Phillip Compeau), and “Learning Algorithms through Programming and Puzzle Solving” (with Alexander Kulikov). He co-developed the Bioinformatics and Data Structure and Algorithms online specializations on Coursera with nearly a million enrollments since 2014.
Host: Prof. Ron Shamir, School of Computer Science